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On 11 July 2011, alongside Lazar Marković, Ninković signed his first professional contract with Partizan, on a five-year deal.[3][4] He made his official debut for the club in the second leg of the second qualifying round for the UEFA Champions League on 19 July 2011, coming on as a substitute for Zvonimir Vukić, against Shkëndija.[5] Ninković made his league debut against Rad on 31 March 2012.

Ninković surpassed Stevan Jovetić as youngest Partizan captain ever on October 31, 2012. Ninković was 17 years, 10 months and 12 days old. [8] He held this honour until he was surpassed by Andrija Živković.

"God gave him an enormous talent and an unbelievable feel for dribbling...He's our Zinedine Zidane and when the time comes, I'm sure he will become the most valuable player in the history of Serbian football."